So FWIW: Airline agents are indeed permitted within the CBP/Immigration/FIS area if they have a Zone 2 CBP seal (Typically a black CBP seal on their badge). This is determined by the Airline in conjunction with CBP, extra steps are taken with an elevated background check & additional scrutiny by CBP to grant this access - CBP usually limits the amount of "Black Seals" that any Airline or ground handler may have & they don't take it lightly.

While many airports and CBP zones vary, for the most part, CBP Zone 1 seals (Red) are granted to anyone working within the footprint of the aircraft and Zone 2 seals (black) are given to those with special need to access the actual screening areas, Jet bridge, FIS, etc.(every airport varies depending upon how the Port Director wants to control access).

At the end of the day, ​​​​​​​It sounds like you just ran into an overly zealous employee who didn't know regs. I'd chalk it up to a lack of training, or maybe this person just wanted to be an authoritarian type ... dunno.​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​